Cyclin-dependent kinase 5 (Cdk5) is predominantly expressed in the nervous system. Though it is expressed in non- neuronal cell and binds with cyclins but its activity is predominantly found in post mitotic neurons due to its binding to neuron specific molecules P35 and P39. It is involved in neuronal migration, synaptic transmission, and survival. Cdk5,a multifunctional neuronal kinase (targeting proteins from neuronal differentiation to synaptic function), is tightly regulated when complexed with p35, its co-activator. It is one of several kinases that phosphorylate neurofilaments and tau. Its diverse roles stem, in part, from its cross-talk interactions with other kinases in signal transduction networks underlying neuronal cell survival, growth and differentiation. We have shown, for example, that Cdk5 down regulates MAPKs and JNKs and up regulates PI3Ks. These results suggest that Cdk5 normally modulates the intensity of response of other kinases to specific signals underlying neuronal survival. The role of Cdk5 in synaptic transmission is mediated by regulating the cellular functions of presynaptic proteins such as synapsin, Munc18, and dynamin 1. Its multifunctional role at the synapse is complex and probably involves other novel substrates.In our previous studies we have demonstrated neuronal stress modulates Cdk5 activity. Since glucocorticoids are the major end effectors of stress response, play an essential role in the homeostasis of the central nervous system (CNS) and contribute to memory consolidation and emotional control through their intracellular receptors, the glucocorticoid and mineralocorticoid receptors. This raises the possibility that Cdk5 may modulate the behavior of these receptors. Indeed we found, Cdk5 phosphorylates and modulates the transcriptional activity of both glucocorticoid and mineralocorticoid receptor and regulates expression of brain-derived neurotrophic factor. Aldosterone and dexamethasone, respectively, increased and suppressed mRNA/protein expression of brain-derived neurotrophic factor (BDNF) in rat cortical neuronal cells, whereas the endogenous glucocorticoid corticosterone showed a biphasic effect. Cdk5 enhanced the effect of aldosterone and dexamethasone on BDNF expression. Because this neurotrophic factor plays critical roles in neuronal viability, synaptic plasticity, consolidation of memory, and emotional changes, we propose that the activation of CDK5 may modulate the transcriptional activity of the glucocorticoid receptors and regulate the expression of BDNF and thus influence these functions. Normally, Cdk5 activity is tightly regulated but under conditions of neuronal stress it is deregulated leading to hyperactivity, neuronal pathology and cell death. Accordingly, Cdk5 has been implicated in certain neurodegenerative disorders such as Alzheimer's Disease (AD). A model of Cdk5s role in neurodegeneration suggests that a stress-induced influx of calcium ions into neurons activates calpain, a Ca++- activated protease, which cleaves p35 into p25 and a p10 fragment. p25, in turn, forms a more stable Cdk5/p25 hyperactive complex, that hyperphosphorylates tau and other neuronal cytoskeletal proteins, and induces cell death. Indeed, increased levels of p25 and Cdk5 activity have been reported in AD brains. That p25 may be toxic comes from studies of cortical neurons treated with Abeta-amyloid peptide,a key marker of AD pathology, where p35 is converted to p25 accompanied by hyper-activated Cdk5, tau and neurofilament hyperphosphorylation and apoptosis. Expression of the Cdk5/p25 complex seems to be primarily responsible for the tau and neurofilament pathology and suggests that a therapeutic approach directed specifically at this target might prove successful. For most of these studies, however, the focus has been amon various laboratories around world on aminothiazol compounds resembling roscovitine, a kinase inhibitor that ccompetes with the ATP binding site in Cdk5 and other kinases. These drugs do not act specifically on Cdk5/p25 but also inhibit Cdk5/p35 and other kinases essential for normal development and function. This could be responsible for serious secondary side effects and thereby compromise any therapeutic value. Our approach to this problem, however, is based on earlier studies where we identified a peptide of 125 amino acid (aa) residues of p35 (CIP) that inhibited Cdk5/p25 activity and rescued cortical neurons from induced apoptosis without affecting Cdk5/p35 activity. This approach might prove to be a more effective way to suppress deregulated Cdk5/p25 hyperactivity inducing neurodegenerative pathology. For a therapy to be effective, however, it must be small enough molecule to pass the blood-brain barrier;a large peptide of 125 residues may be problematic, to say the least. For that reason, we set out to produce a smaller peptide of CIP with equivalent specificity. Based on an analysis of Cdk5/p25 crystal structure and molecular dynamics, several smaller peptides were generated and tested. We identified a novel 24 amino acid peptide, called p5, that more effectively inhibited Cdk5/p25 activity in cortical neurons than CIP without affecting endogenous Cdk5/p35, nor other Cdks. The small size and specificity of p5 inhibition make it an excellent candidate for therapeutic trials in animal models of AD and other neurodegenerative disorders associated with Cdk5 deregulation. This may provide a possible new and novel therapeutic route for intervention to prevent or reduce the neurodegenerative pathology induced by Cdk5 deregulation. The Cdks ligand binding mechanisms are not understood , although a large numbers of molecules including various inhibitors and activators have been used to study their effects on its activity. In a recent study we have used crystal structure of the Cdk5/p25 complex to understand the possible molecular mechanisms of the ligand binding, specificity, and regulation of the kinase using comparative molecular dynamics simulations under physiological conditions. This study provides new insight on the mechanisms that modulate such processes, which may be exploited to control pathological activation by p25. The structural changes observed in the kinase are stabilized by a network of interactions involving highly conserved residues within the cyclin-dependent kinase (cdk) family. Collective motions of the proteins (cdk5, p25, and inhibitor,CIP) and their complexes are identified by principal component analysis, revealing two conformational states of the activation loop upon p25 complexation, which are absent in the uncomplexed kinase and not apparent from the crystal. Simulations of the uncomplexed inhibitor CIP show structural rearrangements and increased flexibility of the interfacial loop containing the critical residue E240, which becomes fully hydrated and available for interactions with one of several positively charged residues in the kinase. These changes provide a rationale for the observed high affinity and enhanced inhibitory action of CIP when compared to either p25 or the physiological activators of cdk5, p35.